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Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator. Session: Managing Ecological Data for Effective Use and Reuse. Patrice Seyed 1,2 , Katherine Chastain 1 , and Deborah McGuinness 1

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linking disparate datasets of the earth sciences with the semanteco annotator

Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator

Session: Managing Ecological Data for

Effective Use and Reuse

Patrice Seyed1,2, Katherine Chastain1, and Deborah McGuinness1

1Tetherless World Constellation, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180

2DataONE, University of New Mexico, 1 University Boulevard N.E., Albuquerque, NM 87131

  • Introduction
  • Semantics and Linked Data
  • Use Case: SemantEco
  • SemantEco Annotator
    • Concept
    • Getting started
    • Overview
  • Ontologies
  • Capabilities
  • Integration with Semantic Applications
  • Future Work
  • Quick Look Video
  • Summary
  • How can we take datasets from different sources and make them
    • Easy to search and to discover?
    • Easy to use and to re-use?
    • Easy to integrate with each other for visualization and other applications?
semantics and linked data
Semantics and Linked Data
  • We need a way to describe the relationshipsbetween tabular data columns…

Linked-data formats such as the Resource Description Framework (RDF) capture such relationships in subject-predicate-object triples.

  • … and we need a method of description that is both standardized and machine-readable.

Communities can develop, use, and reuse common vocabulary with ontologies, expressed in a computer-readable format: the Web Ontology Language (OWL)

semantics and linked data1
Semantics and Linked Data
  • Linked format aids interoperability, making it easier to share.
  • Use existing URI’s to refer to well-defined entities and concepts:
    • How do you make sure that everyone using your data understands that the string “NY” refers to the US state of New York?
    • What more can you learn if you can easily discover other datasets that also refer to the US state of New York?
use case semanteco
Use Case: SemantEco
  • SemantEco is a data visualization environment that allows a user to explore ecological data through a map-based interface.
  • Data comes from a variety of sources:
    • Federal, such as the USGS, EPA.
    • Local, such as the Darrin Freshwater Institute of Upstate New York.
    • … each with different notations and best-practices for gathering and recording.
  • Represent data independent of the schema by which it was recorded
  • This enables comparisons across data from different sources
  • In SemantEco, we look at Measurements:
    • Water quality
    • Air quality
    • Birds
    • Fish
semanteco annotator
SemantEco Annotator

Allows a user to:

  • Translate data into linked-data formats such as RDF:
    • Linked data triples describe how columns in a data table relate to each other, and to the data in that column.
    • OWL ontologies provide standard vocabularies for describing data these relationships.
    • Resulting enriched RDF data can be used immediately within RDF stores / hosted as LD.
  • OR to utilize semantics to annotate data:
    • Column headers correspond to OWL properties
    • Data cell values can correspond to OWL classes or datatypes
    • Organizational best-practices and terminology can be defined in the data files themselves.
provenance and metadata
Provenance and Metadata
  • Annotator asks the user to provide metadata about the dataset.
  • This is also becomes part of the final RDF, facilitating the dataset’s discoverability.
semanteco annotator1
SemantEco Annotator

-- Tabular data view

semanteco annotator2
SemantEco Annotator

--Ontology loader

-- Ontology facets

semanteco annotator3
SemantEco Annotator

-- Global settings

semanteco annotator4
SemantEco Annotator

-- Drag-and-drop to make assignments

-- Work directly on tabular data

  • Load one or more ontologies from the dropdown menu.
  • Or import from a URI.
  • Annotator also maintains a list of recent imports for re-use.
  • Provide a definition for “Accession Code”
  • Specify which standard was used to record the Date
  • Group “Lake Name”, “Z Max” and “Sample Z” together as a single entity: the location where the sample was taken
  • Make explicit that “NH4+” is the same thing as “Ammonium”, and that the units (mg/L) apply to each number in that column.
integration with semantic applications
Integration with Semantic Applications
  • Identify application’s requirements:
      • Eg., a piece of data with lat-long coordinates can be plotted on a map.
  • We brought in data from the Darrin Freshwater Institute containing water quality data for lakes in Upstate New York, augmenting existing data from the U.S. Geological Survey.

“Big Moose Lake”

integration with semantic applications1
Integration with Semantic Applications
  • Linking data to well-defined entities and concepts by URI enhances searchability.






“New York State”

“New York”

future work
Future Work
  • Automatic mappings directed to a particular graph closed under a predicate/object pair, use of OWL domain and range restriction axioms to guide the user in vocabulary selection decisions
  • Use of OWL class definitions to enable a top-down approach for modeling data
  • Ability to load enhancement files, both to facilitate translation of multiple similar datasets, and to make corrections easier.
  • Construction of a platform for better management of linked data, within which the Annotator plays a vital role.
  • Use of application requirements to create “templates” for new data sources to be integrated more easily.
  • “SemantEco Annotator” component for ease of translation into RDF
  • Multi-purposed for translation, annotation, and generalized mapping.
  • A Part of a Future “Suite” that couples Annotation and Search
semanteco annotator project page
SemantEco Annotator Project Page

Want more info? Interested in collaborating?See Evan Patton or email Deborah

We also have a project page with screenshots and demonstration videos:

  • Rensselaer Polytechnic Institute
  • Tetherless World Constellation at RPI
  • DataONE
semanteco more info
SemantEco: More Info

For additional information about SemantEco:

“Addressing the Challenges of Multi-Domain Data Integration with the SemantEco Framework”

Friday @ 10:35am, IN52B-02.

E.W. Patton; P. Seyed; D.L. McGuinness